dbxreport

 

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Function

Validate index and report internals for dbx databases

Description

dbxreport reports statistics for the index fields of a database.

Algorithm

The index directory is, by default, the index directory af an installed database.

dbxreport reads the index file, reporting on the file name, the number of index terms, the depth of the index tree, statistics of internal page types and the free space in an uncompressed index.

Usage

Here is a sample session with dbxreport


% dbxreport -indexdir . 
Validate index and report internals for dbx databases
EMBOSS database name: embl
Index fields [id]: id,acc
Output file [embl.dbxreport]: 

Go to the output files for this example

Command line arguments

Validate index and report internals for dbx databases
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-dbname]            string     EMBOSS database name (Any string from 2 to
                                  19 characters, matching regular expression
                                  /[A-z][A-z0-9_]+/)
  [-fields]            string     [id] A list of index fields separated by
                                  spaces or commas. (Any string)
   -outfile            outfile    [*.dbxreport] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -indexdir           directory  Index directory (optional)
   -fullreport         boolean    [N] Write full details to debug file

   Associated qualifiers:

   "-indexdir" associated qualifiers
   -extension          string     Default file extension

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-dbname]
(Parameter 1)
string EMBOSS database name Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/ Required
[-fields]
(Parameter 2)
string A list of index fields separated by spaces or commas. Any string id
-outfile outfile Output file name Output file <*>.dbxreport
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-indexdir directory Index directory (optional) Directory  
-fullreport boolean Write full details to debug file Boolean value Yes/No No
Associated qualifiers
"-indexdir" associated directory qualifiers
-extension string Default file extension Any string  
"-outfile" associated outfile qualifiers
-odirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

dbxreport reads index files created by any of the EMBOSS 'dbx' indexing applications.

Output file format

The output is a text report of index statistics.

Output files for usage example

File: embl.dbxreport

Index 'id' (.xid)
  compressed:  Yes (Compressed)
   cachesize: 2000 (Size of primary cache)
seccachesize: 2000 (Size of secondary cache)
    pagesize: 2048 (Page size)
 secpagesize:  512 (Secondary page size)
   pagecount:    3 (Primary page count)
   pagecount:    0 (Secondary page count)
    refcount:    0 (Number of reference files)
       order:   71 (Tree order)
      sorder:   99 (Order of secondary tree)
       level:    0 (Level of tree)
      slevel:    0 (Level of secondary tree)
        fill:   56 (Entries per bucket)
       sfill:  169 (Entries per secondary bucket)
    keylimit:   15 (Max key size)
     idlimit:    0 (Max secondary id size)
       count:    6 (Unique entries in index)
   fullcount:    6 (Total entries in index)
Identifier index 'id' index found with 3 pages
      COUNT: 6
   COUNTALL: 6
       root: 1
     bucket: 2
...       keys: 1
...      bkeys: 6
...   total_size: 6144
...    freespace: 5871, 95.6% of uncompressed 6144
      FOUND: 6
   FOUNDALL: 6
Index 'acc' (.xac)
  compressed:  Yes (Compressed)
   cachesize: 2000 (Size of primary cache)
seccachesize: 2000 (Size of secondary cache)
    pagesize: 2048 (Page size)
 secpagesize:  512 (Secondary page size)
   pagecount:    3 (Primary page count)
   pagecount:    3 (Secondary page count)
    refcount:    0 (Number of reference files)
       order:   71 (Tree order)
      sorder:   22 (Order of secondary tree)
       level:    0 (Level of tree)
      slevel:    0 (Level of secondary tree)
        fill:   56 (Entries per bucket)
       sfill:   41 (Entries per secondary bucket)
    keylimit:   15 (Max key size)
     idlimit:    0 (Max secondary id size)
       count:    7 (Unique entries in index)
   fullcount:    9 (Total entries in index)
Identifier index 'acc' index found with 6 pages
      COUNT: 7
   COUNTALL: 9
       root: 1
    numroot: 1
     bucket: 2
  numbucket: 2
...       keys: 2
...      bkeys: 7
...      bdups: 1
...      bxtra: 2
...      nkeys: 3 (0)
...   total_size: 7680
...    freespace: 7236, 94.2% of uncompressed 7680
      FOUND: 7
   FOUNDALL: 9

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
dbiblast Index a BLAST database
dbifasta Index a fasta file database
dbiflat Index a flat file database
dbigcg Index a GCG formatted database
dbxcompress Compress an uncompressed dbx index
dbxedam Index the EDAM ontology using b+tree indices
dbxfasta Index a fasta file database using b+tree indices
dbxflat Index a flat file database using b+tree indices
dbxgcg Index a GCG formatted database using b+tree indices
dbxobo Index an obo ontology using b+tree indices
dbxresource Index a data resource catalogue using b+tree indices
dbxstat Dump statistics for dbx databases
dbxtax Index NCBI taxonomy using b+tree indices
dbxuncompress Uncompress a compressed dbx index

Author(s)

Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None